Streamlined Data Analysis Pipeline for Deep Sequence-Coupled Biopanning Identification of Pathogen-Specific Antibody Responses in Serum

Javier Leo; Susan B Core; Kathryn M Frietze

doi:10.1007/978-1-0716-3279-6_23

Streamlined Data Analysis Pipeline for Deep Sequence-Coupled Biopanning Identification of Pathogen-Specific Antibody Responses in Serum

Methods Mol Biol. 2023:2681:399-406. doi: 10.1007/978-1-0716-3279-6_23.

Authors

Javier Leo¹, Susan B Core¹, Kathryn M Frietze^{2

3}

Affiliations

¹ Department of Molecular Genetics and Microbiology, School of Medicine, University of New Mexico, Albuquerque, NM, USA.
² Department of Molecular Genetics and Microbiology, School of Medicine, University of New Mexico, Albuquerque, NM, USA. kfrietze@salud.unm.edu.
³ Clinical and Translational Science Center, University of New Mexico Health Sciences, Albuquerque, NM, USA. kfrietze@salud.unm.edu.

PMID: 37405661
DOI: 10.1007/978-1-0716-3279-6_23

Abstract

Deep sequence-coupled biopanning (DSCB) is a powerful tool that couples affinity selection of a bacteriophage MS2 virus-like particle peptide display platform with deep sequencing. While this approach has been used successfully to investigate pathogen-specific antibody responses in human sera, data analysis is time-consuming and complicated. Here, we describe a streamlined data analysis method for DSCB using MATLAB, expanding the potential for this approach to be deployed rapidly and consistently.

Keywords: Affinity selection; Antibodies; Deep sequencing; MATLAB; Pathogens; Phage display; Serum; Virus-like particle.

MeSH terms

Antibodies / blood
Antibody Formation
Bioprospecting / methods
Cell Surface Display Techniques / methods
High-Throughput Nucleotide Sequencing* / methods
Software*

Substances

Antibodies